Hi , Hirdesh Kumar:
I learned the basic skills about amber from the online AMBER TUTORIALS , and in the TUTORIAL B1 ,things are did as the order that I described before . Actually , I have no idea about the difference when things are did in contrary order.
-Sun
At 2013-01-22 17:04:07,"Hirdesh Kumar" <hirdesh.iitd.gmail.com> wrote:
>One Na+ as counterion was added to the ligand for neutralizing the nagetive
>charge , then the systen was solvated in TIP3P water model with the water
>buffer being 8 angstroms .
>
>
>Usually we first solvate the system and then replace water molecule
>with counterion
>to neutralize the system. Why did you do other way around?
>
>
>On Tue, Jan 22, 2013 at 9:58 AM, Sun <sunbintyy.163.com> wrote:
>
>> Dear all:
>>
>> I have a ligand which comprises of 36 atoms and its net charge is -1. I
>> have generated the force field parameter files ,i.e., prepin and frcmod
>> files, for the ligand with antechamber correctly. One Na+ as counterion was
>> added to the ligand for neutralizing the nagetive charge , then the systen
>> was solvated in TIP3P water model with the water buffer being 8 angstroms .
>> The system was then subjected to a minimization with the input file reads
>> as following :
>> &cntrl
>> imin=1,maxcyc=2000,ncyc=1500,
>> cut=8.0,ntb=1,
>> ntc=2,ntf=2,
>> ntpr=50,
>> drms=0.05
>> ntr=1,
>> restraint_wt=2.0,
>> restraintmask=":1"
>> /
>> There were two points seemed weird in the output file of the
>> minimizaton : First , the minimization finished without achieving the
>> criteria " drms < 0.05" nor the maxcyc was reached ( it stopped at step
>> 1600 with the message "RESTARTED DUE TO LINMIN FAILURE" ) . Second, the
>> energy information about the previous 1550 steps which were accomplished
>> were exactly the same, i.e., from NSTEP1 to NSTEP2, nothing changed. it
>> seems that the minimization does not do any effect at all .
>>
>> So, could anyone give me some help or advice ? I am very appreciated for
>> your help.
>>
>> -Sun
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 22 2013 - 01:30:05 PST
